Experiment metadata is missing from the final result - Githubissues

bokulich-lab / q2-fondue

Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere

BSD 3-Clause "New" or "Revised" License

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Experiment metadata is missing from the final result #85

Closed misialq closed 2 years ago

misialq commented 2 years ago

Steps to reproduce:

use get-metadata action to fetch metadata for project PRJNA13694
look at the result: compare to metadata available here: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRR066138 (one run from that project)

Expected result:

all metadata fields available in the Run Browser should be present in the table

Actual result:

some metadata are missing (e.g.: Sample Location or Temperature)

Note: We are not parsing the experiment metadata - check here: https://github.com/bokulich-lab/q2-fondue/blob/eb9ee932fc753311510e332a290d0a1f8492cb1f/q2_fondue/entrezpy_clients/_efetch.py#L246-L270

versus run metadata: https://github.com/bokulich-lab/q2-fondue/blob/eb9ee932fc753311510e332a290d0a1f8492cb1f/q2_fondue/entrezpy_clients/_efetch.py#L303